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Microorganisms (Bacteria and Archaea) in the marine cavity beneath the McMurdo Ice Shelf, Antarctica

Citation

Vick-Majors T, Achberger A, Santibanez P, Dore J, Hodson T, Michaud A, Christner B, Mikucki J, Skidmore M, Powell R, Adkins P, Brabante C, Mitchell A, Scherer R, Priscu J, Sweetlove M (2019). Microorganisms (Bacteria and Archaea) in the marine cavity beneath the McMurdo Ice Shelf, Antarctica. Version 1.1. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/vd2gib accessed via GBIF.org on 2022-05-16.

Description

Amplicon sequencing dataset (Illumina MiSeq) of Bacteria and Archaea (16S) in the marine cavity beneath the McMurdo Ice Shelf, Antarctica

Sampling Description

Study Extent

After drilling through the Ice sheet (56m), water samples were taken from the marine cavity beneath the McMurdo Ice Shelf, Antarctica

Sampling

A discrete water sample for nucleic acid extraction was collected in situ at 850 m with a Large Volume Water Transfer System (WTS-LV; McLane Research Laboratories, East Falmouth, Massachusetts). This system was fitted with a stacked 143 mm diameter filter housing that allowed the sample to be size fractionated into 10 um, 3 um, and 0.2 um classes (Supor Membrane filters were used; Pall). This system allowed us to concentrate 295 L of seawater on 142 mm filters during a 4 h in situ deployment. An additional discrete water sample (300 mL) from 30 m was obtained for nucleic acid extraction from a 10 L Niskin bottle sample that was fil- tered through a 47 mm 0.2 um Supor membrane filter (Pall). Filters from the WTS-LV were preserved as described previ- ously (Christner et al. 2014) while the entire 47 mm filter from the 30 m sample was placed in a 7 mL cryovial and preserved with 7 mL of a solution of 40 mM EDTA pH 8.0, 50 mM Tris pH 8.3, and 0.73 M Sucrose to prevent cell lysis during storage.

Method steps

  1. Nucleic acids were extracted from the 10 um, 3 um, and 0.2 um filters from 850 m and the 0.2 um filter from 30 m using a MO BIO PowerWater DNA Isolation Kit according to the manufactures instructions. The V4 hypervariable region of the small subunit (SSU) rRNA gene was amplified using the primers 515F and 806R (Caporaso et al. 2012) and sequenced on an Illumina MiSeq as described by Christner et al. (2014).

Taxonomic Coverages

Bacteria and Archaea (16S ssu rRNA gene)
  1. Bacteria
    common name: bacteria rank: domain
  2. Archaea
    common name: Archaea rank: domain

Geographic Coverages

the marine cavity beneath the McMurdo Ice Shelf, Antarctica

Bibliographic Citations

  1. Vick-Majors T. J., Achberger A., Santibáñez P., Dore J. E., Hodson T., Michaud A. B., et al. (2016). Biogeochemistry and microbial diversity in the marine cavity beneath the McMurdo Ice Shelf, Antarctica. Limnol. Oceanogr. 61 572–586. 10.1002/lno.10234  - doi: 10.1002/lno.10234

Contacts

Trista Vick-Majors
originator
Montana State University
Bozeman
US
Amanda Achberger
originator
Louisiana State University
Baton Rouge
US
Pamela Santibanez
originator
Montana State University
Bozeman
US
John Dore
originator
Montana State University
Bozeman
US
Timothy Hodson
originator
Northern Illinois University
DeKalb
US
Alexander Michaud
originator
Montana State University
Bozeman
US
Brent Christner
originator
Louisiana State University
Baton Rouge
US
Jill Mikucki
originator
Middlebury College
Middlebury
US
Mark Skidmore
originator
Montana State University
Bozeman
US
Ross Powell
originator
Northern Illinois University
DeKalb
US
Peyton Adkins
originator
Louisiana State University
Baton Rouge
US
Carlo Brabante
originator
University of Venice
Venice
IT
Andrew Mitchell
originator
Aberystwyth University
Aberystwyth
GB
Reed Scherer
originator
Northern Illinois University
DeKalb
US
John Priscu
originator
Montana State University
Bozeman
US
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute of Natural Science
Rue Vautier 29
Brussels
1000
email: msweetlove@naturalsciences.be
John Priscu
administrative point of contact
Montana State University
Bozeman
US
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